{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jule Bäcker"],"organism":["Danio rerio"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16477"],"description":["In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to DNOC (CAS 534-52-1). Zebrafish embryos were exposed to DNOC according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions inv"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Illumina HiSeq 4000 sequencing System was employed to obtain 30 million 50 bp single-read raw reads per sample.","Sample Treatment - three zebrafish embryos replicate groups originating from three different tanks were exposed to each of two sub-lethal concentrations of DNOC (high exposure and low exposure concentrations) in addition to untreated control groups.","Library Construction - RNA libraries were prepared from RNA extracts with RNA integrity number (RIN) values > 8 using poly(A) RNA purification and the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, USA).","Sample Collection - at the end of exposure, 10 Embryos were euthanized on ice then homogenised in lysis buffer using Lysing Matrix D ceramic beads in FastPrep-24 homogeniser (MP Biomedicals, Irvine, USA) at 5 m/s speed for 45 seconds.","Nucleic Acid Extraction - simutaneous RNA and protein extraction was performed from the homogenised samples using Macherey & Nagel RNA/protein extraction kit.","Growth Protocol - Zebrafish embryos were exposed to DNOC for 96 hours according to OECD test guidelines No. 236 at 26 ± 1 °C and a light/dark cycle of 14:10 hours."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - adapter sequences were removed using Trimomatic, and alignment of the sequences to the Danio rerio reference genome (GRCz11) was performed using the STAR aligner (v.2.5.2a), followed by read counting with featureCounts (v1.5.0-p1) to obtain count per gene tables.","Data Transformation - the count per gene tables obtained from featureCounts (v1.5.0-p1) were compiled in R (v 4.0.5) in one count matrix (DNOC_2_CountMatrix.txt) where rows correspond to genes and columns to the sample. Only genes with a minimum sum of N counts across N samples (rowSums >= N) were kept for further downstream analysis. Genes with less than 9 counts were excluded, and count normalization DESeq2 (v1.26.0) to obtain the normalized count table (DNOC_DESeqNormCounts). Differential expression analysis on the normalized counts was performed using DEseq2 and the analysis script is publicly available in: https://github.com/hreinwal/DESeq2Analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["RNA-seq of coding RNA"],"species":["Danio rerio"],"pubmed_authors":["Cimin Kalali","Fatma Marghany","Jule Bäcker","Sebastian Eilebrecht","Henner Hollert","Hannes Reinwald","Christoph Schäfers","Julia Alvincz","Pragya Thapaliya"],"additional_accession":[]},"is_claimable":false,"name":"mRNA-Seq of Danio rerio exposed to different concentrations of dinitro-ortho-cresol (DNOC) against untreated control groups","description":"In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to DNOC (CAS 534-52-1). Zebrafish embryos were exposed to DNOC according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions inv","dates":{"release":"2026-09-30T00:00:00Z","modification":"2026-09-30T01:00:43.46Z","creation":"2025-12-22T19:24:57.577Z"},"accession":"E-MTAB-16477","cross_references":{"ENA":["ERP187055"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}